X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-reference.html;h=b2e29e925f62d2b2deda9cf5e55a31802e911d31;hb=56ce5cb6fd0b54f831cf35859886cd69a7f522a3;hp=3532af4989b7137bb1e076c58e22a68b90dd514b;hpb=3778008766299b5db71d77e8530a9c0fe9b6916d;p=jalview.git diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html index 3532af4..b2e29e9 100644 --- a/help/help/html/features/clarguments-reference.html +++ b/help/help/html/features/clarguments-reference.html @@ -35,7 +35,6 @@
‑‑headless
--output
, --image
or --structureimage
) then headless mode will be assumed. If you don't want this behaviour use --gui
.
+ If you use a command line argument to specify an output file of some kind (‑‑output
, ‑‑image
or ‑‑structureimage
) then headless mode will be assumed. If you don't want this behaviour use ‑‑gui
.
‑‑gui
--gui
takes precedence over --headless
.‑‑gui
takes precedence over ‑‑headless
.phylip
(phy
),
jalview
(jvp, jar
).
+ -
(a single hyphen). In this case all STDOUT messages will instead go to STDERR. If no format
is supplied then Fasta will be assumed.
format=name
‑‑mkdirs
‑‑output
, ‑‑image
or ‑‑structureimage
arguments.
+ biojs
.
type=name,
- textrenderer=name,
- scale=number,
- width=number,
- height=number
+
+ type=name,
+
+ textrenderer=name,
+
+ scale=number,
+
+ width=number,
+
+ height=number,
+
+ imagecolour=name
+
+
‑‑structureimage filename
‑‑structureimage
filename will output a file for each ‑‑structureimage
that has been applied to the open alignment window. In this situation, to avoid overwriting the same file with each structure, additional substitutions {structuredirname}
, {structurebasename}
and {structureextname}
are available being substituted with the directory path, file basename and file extension of each structure file. Image formats can be:
+ svg
,
+ png
,
+ eps
.
+
+ type=name,
+
+ textrenderer=name,
+
+ scale=number,
+
+ width=number,
+
+ height=number,
+
+ imagecolour=name
+
+ bgcolour=name
+
‑‑type name
‑‑image
to name. Valid values for name are:
+ ‑‑image
or ‑‑structureimage
to name. Valid values for name are:
svg
,
‑‑textrenderer name
‑‑image
or ‑‑structureimage
. Valid values for name are:
text
,
‑‑scale number
--image
value. If used in conjunction with --width
and --height
then the smallest scaling will be used (scale
, width
and height
provide bounds for the image).
+ ‑‑image
or ‑‑structureimage
. This can also be set as a sub-value modifier to the ‑‑image
or ‑‑structureimage
value. If used in conjunction with ‑‑width
and ‑‑height
then the smallest size will be used (scale
, width
and height
provide bounds for the image).
‑‑width number
--image
value. If used in conjunction with --scale
and --height
then the smallest scaling will be used (scale
, width
and height
provide bounds for the image).
+ ‑‑image
or ‑‑structureimage
. Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image
or ‑‑structureimage
value. If used in conjunction with ‑‑scale
and ‑‑height
then the smallest size will be used (scale
, width
and height
provide bounds for the image).
‑‑height number
--image
value. If used in conjunction with --scale
and --width
then the smallest scaling will be used (scale
, width
and height
provide bounds for the image).‑‑groovy filename
jmol
only)argument | -action | -sub-value modifiers (optional) | -linked (optional) | -||
‑‑structureimage filename |
- Export an image of a 3D structure opened in JMOL. Image formats can be:
- - svg ,
- - png ,
- - eps .
- |
-
- structureimagetype=name,
- |
- ✓ | -||
‑‑structureimagetype name |
- Set the structure image format for the preceding --structureimage. Valid values are:
- - svg ,
- - png ,
- - eps .
- |
- - | ✓ | -||
‑‑structureimagetextrenderer name |
- Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:
- - text ,
- - lineart .
- |
+ Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Applies to the preceding ‑‑image or ‑‑structureimage . Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑scale and ‑‑width then the smallest size will be used (scale , width and height provide bounds for the image). |
✓ | ||
‑‑structureimagescale number |
- Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | +‑‑bgcolour name |
+ Only applies to structure images (opened with jmol structure viewer). Sets the background colour of the preceding ‑‑structureimage . name should be either a named colour (e.g. white , cyan ) known to Jmol, or can be given as a six digit RGB hex string (e.g. ffffff , 00ffff ). This can also be set as a sub-value modifier to the ‑‑structureimage value. |
✓ | |
‑‑structureimagewidth number |
- Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | -- | ✓ | -||
‑‑structureimageheight number |
- Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | +‑‑groovy filename |
+ Process a groovy script in the file for the open alignment. | ✓ |
Move on to a new alignment window. This will ensure ‑‑append will start a new alignment window and other linked arguments will apply to the new alignment window.
- Note that --open already starts a new alignment window for each file it opens.
+ Note that ‑‑open already starts a new alignment window for each file it opens.
|
‑‑substitutions / ‑‑nosubstitutions |
The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
+ {basename} - the filename-without-extension of the currently ‑‑open ed file (or first ‑‑append ed file),
{dirname} , - the directory (folder) name of the currently ‑‑open ed file (or first ‑‑append ed file),
+ {extension} , - the extension of the filename of the currently ‑‑open ed file (or first ‑‑append ed file),
{argfilebasename} - the filename-without-extension of the current ‑‑argfile ,
{argfiledirname} - the directory (folder) name of the current ‑‑argfile ,
+ {structurebasename} - the filename-without-extension of the ‑‑structure file. Only available to ‑‑structureimage .
+ + {structuredirname} , - the directory (folder) name of the ‑‑structure file. Only available to ‑‑structureimage .
+ + {structureextension} , - the extension of the filename of the ‑‑structure file. Only available to ‑‑structureimage .
+ {n} - the value of the index counter (starting at 0).
- {++n} - increase and substitute the value of the index counter,
+ {++n} - increase and substitute the value of the index counter.
+ + {m} - the value of the on-the-fly counter (starting at 0). Only available to ‑‑structureimage .
+ + {++m} - increase and substitute the (incremented) value of the on-the-fly counter. Only available to ‑‑structureimage .
{} - the value of the current alignment window default index.
|
@@ -815,7 +800,7 @@
||||
‑‑allstructures / ‑‑noallstructures |
- Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst --allstructures will continue to operate for a --new alignment, the structure formatting arguments must be set again for each new alignment.
+ Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst ‑‑allstructures will continue to operate for a ‑‑new alignment, the structure formatting arguments must be set again for each new alignment.
|